The 2006 UEFA Intertoto Cup was the first edition after a major change of the competition format. There were only three rounds instead of five, and eleven tournament co-winners qualified for the second qualifying round of the UEFA Cup. Also, for the first time in the modern history of the competition, an outright winner was highlighted from the 11 co-winners of the Cup, with that honour going to the final-round Intertoto winner that advanced farthest in the UEFA Cup. This honour went to Newcastle United.
First round
!colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region
Farul Constanţa won 4–2 on aggregate. ---- Maribor won 8–0 on aggregate. ---- Ethnikos Achna FC won 5–4 on aggregate. ---- NK Zrinjski won 4–1 on aggregate. ---- Dinamo Tbilisi won 8–1 on aggregate. ---- MTZ-RIPO Minsk won 6–4 on aggregate. ---- Nitra won 12–2 on aggregate. ---- Tiraspol won 2–1 on aggregate. ---- Keflavík won 4–1 on aggregate. ---- Dinaburg won 2–1 on aggregate. ---- Tampere United won 8–1 on aggregate. ---- Kalmar FF won 8–1 on aggregate. ---- Shelbourne won 5–0 on aggregate.
---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- 1The match was played at FK Partizan's ground in Belgrade, Serbia, because FK Zeta's ground in Golubovci doesn't meet UEFA standards
2The match was played in Herzliya because Maccabi Petah Tikva's ground in Petah Tikva is undergoing renovations
Second leg
Kayserispor won 4–3 on aggregate. ---- Farul Constanţa won 3–2 on aggregate. ---- Maribor won 4–1 on aggregate. ---- Maccabi Petah Tikva won 4–2 on aggregate. ---- 2–2 on aggregate, Ethnikos Achna won on away goals rule. ---- Grasshoppers won 4–0 on aggregate. ---- Dnipro Dnipropetrovsk won 3–2 on aggregate. ---- SV Ried won 4–1 on aggregate. ---- Tiraspol won 4–1 on aggregate. ---- FC Moscow won 3–0 on aggregate. ---- Kalmar FF won 5–3 on aggregate. ---- OB won 3–1 on aggregate. ---- Lillestrøm won 6–3 on aggregate. ---- Hibernian won 8–0 on aggregate.
Third round
Eleven winning teams qualify for the second qualifying round of 2006–07 UEFA Cup !colspan="5"|Southern-Mediterranean region !colspan="5"|Central-East region !colspan="5"|Northern region ^played on 16 July *After consultations with UEFA, Italian qualifier Palermo was withdrawn by the Italian Football Federation on 6 June 2006. Due to the ongoing match-fixingscandal in Italy, the FIGC could not officially confirm the 2005–06 Serie A standings in time for Palermo to compete in the Intertoto Cup and therefore French club Auxerre replaced Palermo, according to UEFA regulations governing the Intertoto Cup.
First leg
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Second leg
AJ Auxerre won 4–2 on aggregate. ---- Kayserispor won 2–0 on aggregate. ---- Maribor won 3–2 on aggregate. ---- Ethnikos Achna won 4–3 on aggregate. ---- Grasshoppers won 3–2 on aggregate. ---- 2–2 on aggregate, Marseille won on away goals rule. ---- Hertha BSC won 2–0 on aggregate. ---- SV Ried won 4–2 on aggregate. ---- Newcastle United won 4–1 on aggregate. ---- Twente won 3–2 on aggregate. ---- 2–2 on aggregate, OB won on away goals rule.
Overall winners
Eight of the eleven co-winners which entered the UEFA Cup via the Intertoto Cup won their qualifying ties and progressed to the first round proper. Half of these eight survived the first round and entered the group stages, only Newcastle United secured a place in the UEFA Cup Round of 32 and were the last remaining team from the Intertoto Cup – making them the outright winner. They then went on to qualify for the last 16. Captain Scott Parker was presented with a certificate commemorating the triumph at St James Park before their tie with AZ.
